SMTL ID : 8xn3.1

SARS-CoV-2 Omicron HV.1 RBD in complex with human ACE2 (local refinement from the spike protein)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: N.35, Q.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.322 NAG.2: 5 residues within 4Å: Chain A: K.8, N.72, T.74, V.75, Q.78 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.75 Hydrogen bonds: A:K.8 NAG.3: 4 residues within 4Å: Chain A: Q.63, Q.83, N.85, N.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:N.176 NAG.4: 1 residues within 4Å: Chain A: N.414 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.528 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: E.294, V.298, N.304, M.305 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain A: H.356, H.360, E.384 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.356, A:H.360, A:E.384, A:E.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Structure (2024)

Release Date

2024-07-03

Peptides

Angiotensin-converting enzyme 2: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Angiotensin-converting enzyme 2

Spike protein S1

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